Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

Nat Biotechnol. 2012 Feb 12;30(3):253-60. doi: 10.1038/nbt.2122.


RNA editing is a post-transcriptional event that recodes hereditary information. Here we describe a comprehensive profile of the RNA editome of a male Han Chinese individual based on analysis of ∼767 million sequencing reads from poly(A)(+), poly(A)(-) and small RNA samples. We developed a computational pipeline that carefully controls for false positives while calling RNA editing events from genome and whole-transcriptome data of the same individual. We identified 22,688 RNA editing events in noncoding genes and introns, untranslated regions and coding sequences of protein-coding genes. Most changes (∼93%) converted A to I(G), consistent with known editing mechanisms based on adenosine deaminase acting on RNA (ADAR). We also found evidence of other types of nucleotide changes; however, these were validated at lower rates. We found 44 editing sites in microRNAs (miRNAs), suggesting a potential link between RNA editing and miRNA-mediated regulation. Our approach facilitates large-scale studies to profile and compare editomes across a wide range of samples.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Humans
  • Lectins, C-Type / genetics
  • Lectins, C-Type / metabolism
  • MicroRNAs / genetics
  • MicroRNAs / metabolism
  • Poly A / genetics
  • Poly A / metabolism
  • Polymorphism, Single Nucleotide
  • RNA / genetics*
  • RNA / metabolism
  • RNA Editing*
  • Receptors, Cell Surface / genetics
  • Receptors, Cell Surface / metabolism
  • Sequence Analysis, RNA
  • Transcriptome*


  • CLEC2D protein, human
  • Lectins, C-Type
  • MicroRNAs
  • Receptors, Cell Surface
  • Poly A
  • RNA